Hello,
I did Mendelian randomization using this software:
https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf
library(MendelianRandomization)
f=read.table("246LDout272Biobank_Retina.txt",
header=T)> head(f)
rs exposure.beta exposure.se outcome.beta outcome.se
1 rs1029830 0.723525 0.03026430 0.066715400 0.0359278
2 rs1029832 0.723785 0.03029603 0.064105600 0.0359021
3 rs11078374 -0.411789 0.04189295 -0.000376929 0.0406439
4 rs11078382 0.882549 0.14275799 -0.197074000 0.1247720
5 rs1124961 -0.333763 0.05589377 -0.075468600 0.0576012
6 rs1135237 -0.316831 0.05552530 -0.074086200 0.0573111
MRInputObject <- mr_input(bx = f$exposure.beta,bxse = f$exposure.se,by
= f$outcome.beta,byse = f$outcome.se)
EggerObject <- mr_egger(MRInputObject,robust = FALSE,penalized FALSE,correl =
FALSE,distribution = "normal",alpha = 0.05)
MR-Egger method
(variants uncorrelated, random-effect model)
Number of Variants = 246
------------------------------------------------------------------
Method Estimate Std Error 95% CI p-value
MR-Egger 0.115 0.016 0.084, 0.146 3.28e-13
(intercept) -0.010 0.008 -0.025, 0.006 0.226
------------------------------------------------------------------
Residual Standard Error : 1.106
Heterogeneity test statistic = 298.4508 on 244 degrees of freedom,
(p-value = 0.0099)
I^2_GX statistic: 97.2%
Let's say that my exposure is called Retina and my outcome is called
Biobank. Can someone please help me interpret these results in terms
of 'horizontal pleiotropy' as mentioned here:
https://www.ncbi.nlm.nih.gov/pubmed/29771313
Thanks
Ana